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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
2yw2 ATP Phosphoribosylamine--glycine ligase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2yw2 ATPPhosphoribosylamine--glycine ligase / 1.062
3t9e ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.697
3t9f ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.689
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.682
4mam A12N5-carboxyaminoimidazole ribonucleotide synthase / 0.680
1pk8 ATPSynapsin-1 / 0.676
4q4c ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / 0.674
2p0a ANPSynapsin-3 / 0.672
2p2m PRXAcetyl-coenzyme A synthetase / 0.671
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.669
3q1k ADPD-alanine--D-alanine ligase A 6.3.2.4 0.666
5ifi PRXAcetyl-coenzyme A synthetase / 0.660
3fcc ATPD-alanine--poly(phosphoribitol) ligase subunit 1 / 0.658
4r1l ADPPhenylacetate-coenzyme A ligase / 0.656
2p2b PRXAcetyl-coenzyme A synthetase / 0.652
4dca ADPAminoglycoside phosphotransferase / 0.652